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rksn_automate

This repository contains automation code developed for the research paper titled "Exploring Enantioselectivity in Organocatalysis: Insights from Bonding and Energy Decomposition Analyses".

The code automates the TS search method for all the conformers based on the product structure.

Dependencies

  • Python (version >= 3.7 should work fine)
  • No python external library required.
  • Mainly tested with Anaconda Python.
  • Without Anaconda the automation script should run fine but need to change couple of things (see below).

External Programmes

  • Interfaced with ORCA 4.2.1
  • XTB and CREST from Grimme Lab

Installation

  • Clone the rksn_automate repository.

  • Set the absolute path in lib.py def slurm_input(inp_file, jobname) function.

  • This code runs in the SLURM queuing system. A slurm submit script submit.sh is provided. Please change the file accordingly.

  • If other than SLURM queuing system is used change the lib.py def slurm_input(inp_file, jobname) function and modify the submit.sh file. If you are not using Anaconda python, find the proper python interpreter path and modify this two file.

  • In our test system both ORCA and XTB software are set up with the Module system. Load proper version of ORCA and XTB in the submit.sh file. Without the module system also it is easy to set up the automation script.

Running the Script

The run command is provided inside the submit.sh file.

python3 -u ~/rksn_automate/start.py -m start.xyz -r act_atom.txt > output.log

where rksn_automate repo is cloned in the $HOME directory of the user.

The run command required a act_atom.txt file and an optional constrain file. Samples for the files are provided in the repository.

The act_atom.txt file contains the index of the two atoms where bond breaking or forming will happen according to the start.xyz file. The constrain file contains the the Dihedral Constrain if required during the bond scan between the two active atoms. This format of the file is according to the ORCA input file. All the index starts from 0.

The start.py file first do the conformation search using CREST and XTB. This script will generate a path.txt file which will be submitted later automatically for parallel run of the all conformers.

The DFT methods and settings for ORCA runs are provided at the beginning of the lib.py file. The SMD single point methods are also present. You can set up your preferred DFT Functional and basis set here. Change PROCS variable for setting up the number of ORCA parallel processors. The BLOCKS variable determines how many low energy conformers will be taken from the crest conformer search file for the reaction path study.

Contact

For any inquiries or questions regarding the code or research paper, please contact saikat403@gamil.com.